data_4LV7 # _model_server_result.job_id QVegrpCVjMdvu2ywRzCWyA _model_server_result.datetime_utc '2024-11-23 04:48:01' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4lv7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 4LV7 # _exptl.entry_id 4LV7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 83.01 _cell.angle_beta 89.92 _cell.angle_gamma 63.41 _cell.entry_id 4LV7 _cell.length_a 59.763 _cell.length_b 59.353 _cell.length_c 82.232 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LV7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F 1 1 B,G,H,I,J 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 H N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 116 A CYS 82 1_555 A SG CYS 176 A CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 B SG CYS 116 B CYS 82 1_555 B SG CYS 176 B CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc1 A ND1 HIS 354 A HIS 320 1_555 F ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc2 A SG CYS 364 A CYS 330 1_555 F ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc3 A SG CYS 367 A CYS 333 1_555 F ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc4 A NE2 HIS 380 A HIS 346 1_555 F ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc5 A OD1 ASP 441 A ASP 407 1_555 E MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc6 A OG SER 443 A SER 409 1_555 E MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? metalc ? metalc7 D O1B ADP . A ADP 502 1_555 E MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc8 B ND1 HIS 354 B HIS 320 1_555 J ZN ZN . B ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc9 B SG CYS 364 B CYS 330 1_555 J ZN ZN . B ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc10 B SG CYS 367 B CYS 333 1_555 J ZN ZN . B ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc11 B NE2 HIS 380 B HIS 346 1_555 J ZN ZN . B ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc12 G O22 IHP . B IHP 501 1_555 I MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.947 ? metalc ? metalc13 H O2B ADP . B ADP 502 1_555 I MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc14 H O1A ADP . B ADP 502 1_555 I MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.874 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 4LV7 _atom_sites.fract_transf_matrix[1][1] 0.016733 _atom_sites.fract_transf_matrix[1][2] -0.008374 _atom_sites.fract_transf_matrix[1][3] 0.00112 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01884 _atom_sites.fract_transf_matrix[2][3] -0.002573 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.012274 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 IHP A 1 501 500 IHP IHP . D 3 ADP A 1 502 600 ADP ADP . E 4 MG A 1 503 700 MG MG . F 5 ZN A 1 504 800 ZN ZN . G 2 IHP B 1 501 500 IHP IHP . H 3 ADP B 1 502 600 ADP ADP . I 4 MG B 1 503 700 MG MG . J 5 ZN B 1 504 800 ZN ZN . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PB ADP . . . D 3 -9.864 24.614 22.309 1 53.25 ? PB ADP 502 A 1 HETATM 2 O O1B ADP . . . D 3 -8.93 23.442 22.086 1 45.62 ? O1B ADP 502 A 1 HETATM 3 O O2B ADP . . . D 3 -9.351 25.942 21.782 1 48.67 ? O2B ADP 502 A 1 HETATM 4 O O3B ADP . . . D 3 -11.232 24.227 21.796 1 29.71 ? O3B ADP 502 A 1 HETATM 5 P PA ADP . . . D 3 -8.522 25.283 24.774 1 25.55 ? PA ADP 502 A 1 HETATM 6 O O1A ADP . . . D 3 -7.688 26.36 24.119 1 23.36 ? O1A ADP 502 A 1 HETATM 7 O O2A ADP . . . D 3 -7.787 24.012 25.134 1 27.7 ? O2A ADP 502 A 1 HETATM 8 O O3A ADP . . . D 3 -9.878 24.953 23.922 1 33.6 ? O3A ADP 502 A 1 HETATM 9 O O5' ADP . . . D 3 -9.117 25.885 26.147 1 35.82 ? O5' ADP 502 A 1 HETATM 10 C C5' ADP . . . D 3 -9.977 27.031 26.185 1 33.7 ? C5' ADP 502 A 1 HETATM 11 C C4' ADP . . . D 3 -9.477 28.088 27.185 1 34.48 ? C4' ADP 502 A 1 HETATM 12 O O4' ADP . . . D 3 -9.307 27.581 28.528 1 37.8 ? O4' ADP 502 A 1 HETATM 13 C C3' ADP . . . D 3 -8.143 28.734 26.792 1 30.74 ? C3' ADP 502 A 1 HETATM 14 O O3' ADP . . . D 3 -8.31 29.951 26.056 1 24.22 ? O3' ADP 502 A 1 HETATM 15 C C2' ADP . . . D 3 -7.446 29.022 28.113 1 31.58 ? C2' ADP 502 A 1 HETATM 16 O O2' ADP . . . D 3 -7.625 30.383 28.49 1 26.99 ? O2' ADP 502 A 1 HETATM 17 C C1' ADP . . . D 3 -8.13 28.144 29.14 1 30.94 ? C1' ADP 502 A 1 HETATM 18 N N9 ADP . . . D 3 -7.182 27.048 29.426 1 35.16 ? N9 ADP 502 A 1 HETATM 19 C C8 ADP . . . D 3 -6.996 25.978 28.624 1 35.62 ? C8 ADP 502 A 1 HETATM 20 N N7 ADP . . . D 3 -6.069 25.128 29.13 1 36.24 ? N7 ADP 502 A 1 HETATM 21 C C5 ADP . . . D 3 -5.636 25.666 30.286 1 35.47 ? C5 ADP 502 A 1 HETATM 22 C C6 ADP . . . D 3 -4.661 25.279 31.33 1 37.04 ? C6 ADP 502 A 1 HETATM 23 N N6 ADP . . . D 3 -3.945 24.136 31.228 1 30.14 ? N6 ADP 502 A 1 HETATM 24 N N1 ADP . . . D 3 -4.511 26.12 32.38 1 38.21 ? N1 ADP 502 A 1 HETATM 25 C C2 ADP . . . D 3 -5.219 27.262 32.488 1 33.76 ? C2 ADP 502 A 1 HETATM 26 N N3 ADP . . . D 3 -6.124 27.673 31.583 1 37.36 ? N3 ADP 502 A 1 HETATM 27 C C4 ADP . . . D 3 -6.37 26.934 30.477 1 35.32 ? C4 ADP 502 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 390 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 27 #